BRAD V3.0: an upgraded Brassicaceae database.

Brassicaceae / classification Databases, Genetic Genome, Plant / genetics Genomics Phylogeny Synteny / genetics

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
07 01 2022
Historique:
accepted: 19 10 2021
revised: 14 10 2021
received: 13 09 2021
pubmed: 11 11 2021
medline: 22 2 2022
entrez: 10 11 2021
Statut: ppublish

Résumé

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

Identifiants

DOI: 10.1093/nar/gkab1057 PMID: 34755871 PMC: PMC8728314
pubmed: 34755871
pii: 6424756
doi: 10.1093/nar/gkab1057
pmc: PMC8728314
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

D1432-D1441

Informations de copyright

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Haixu Chen (H)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Tianpeng Wang (T)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Xiaoning He (X)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Xu Cai (X)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Runmao Lin (R)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Jianli Liang (J)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Jian Wu (J)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.

Graham King (G)

Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia.

Xiaowu Wang (X)

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.
ORCID: 0000-0001-6753-227X

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Brassicaceae › BRAD V3.0: an upgraded Brassicaceae database.
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › BRAD V3.0: an upgraded Brassicaceae database.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › BRAD V3.0: an upgraded Brassicaceae database.
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › BRAD V3.0: an upgraded Brassicaceae database.
questionsmedicales.fr › Sciences de l'information › Phylogenèse › BRAD V3.0: an upgraded Brassicaceae database.
questionsmedicales.fr › Phénomènes génétiques › Similitude de séquences › Similitude de séquences d'acides nucléiques › Synténie › BRAD V3.0: an upgraded Brassicaceae database.